/*===========================================================================
*
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*               National Center for Biotechnology Information
*
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*  terms of the United States Copyright Act.  It was written as part of
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#ifndef _h_pileup_options_
#define _h_pileup_options_

#ifdef __cplusplus
extern "C" {
#endif

#include "ref_regions.h"
#include "cmdline_cmn.h"

typedef struct pileup_options
{
    common_options cmn;     /* from cmdline_cmn.h */
    bool process_dups;
    bool omit_qualities;
    bool read_tlen;
    bool no_skip;
    bool show_id;
    bool div_by_spotgrp;
	bool depth_per_spotgrp;
    bool use_seq_name;
    uint32_t minmapq;
    uint32_t min_mismatch;
    uint32_t merge_dist;
    uint32_t source_table;
    uint32_t function;  /* sra_pileup_samtools, sra_pileup_counters, sra_pileup_stat, 
                           sra_pileup_report_ref, sra_pileup_report_ref_ext, sra_pileup_debug, etc */
    struct skiplist * skiplist;     /* from ref_regions.h */
} pileup_options;


#ifdef __cplusplus
}
#endif

#endif /*  pileup_options_ */
